Ideally, everything I read begins with a BibDesk entry prepared first – in practice I read a lot on iOS first, then convert PDF annotations to Skim annotations & create the citation and links later. Once I’m done reading the PDF in Skim, another applescript automatically extracts all the notes to the clipboard, ready to paste into Ulysses. It autofiles all my PDFs, and I have scripts to generate a new Ulysses sheet for reading notes from a template, including the citation, and to add corresponding keywords (in Ulysses) and/or MacOS tags (for other files). I use BibDesk, even though I don’t actually write in BibTeX, because I can attach multiple files to each record. It may not seem necessary early in grad school but it will make life much easier in the long term if you start working in it now. The missing piece of the system you describe, though, is a citation manager. It has the advantages of great AppleScript support and a robust templating system so you can get exactly the output you want. The alternative that I’ve been using for the last decade (since before there was native PDF annotation in Preview) is Skim – it’s Mac only with Skim annotations but it imports and exports standard PDF annotations flawlessly. And the Mac version can automatically generate a citation if your article has a valid DOI. It has the advantage of using standard PDF annotations. Highlights for iOS is currently in beta – I have been using it through several beta versions and it’s totally stable at this point, and the developer has been receptive to some of my suggestions about customising the output. PDF Expert’s note exporting is kind of awful, and Readdle hasn’t shown any interest in improving it. I would appreciate any advice from people who have arrived at a satisfying system for this sort of work, particularly as it’s done on iPad. It is also much more difficult than I would prefer to quickly generate a citation to append to these highlights for later reference. The text of the extracted highlights especially is often plagued by broken formatting (errant spaces, carriage returns, etc.) that has proven difficult to resolve in an automated fashion, even using tools like Clean Text. While this works in general, pieces of it often fail in the particular. From there, I use one of the sharing features in PDFE to email a summary of the highlights to myself, which is then funneled into Ulysses for storage (currently in the process of switching this latter stage over to KeepIt, which is obviously more suited for archival purposes). In the current incarnation, I import PDFs into PDF Expert on my iPad Pro for reading, highlighting, and annotation using the Apple Pencil. This workflow is also quite helpful when it comes time for grant or paper writing.ĭespite a great deal of tweaking over the years, alas, I’m still not completely satisfied with this process. One of the practices that I’ve found helpful for retention is storage of highlights I make from papers I read as plain text, usually paired with the relevant citation and, depending on where I choose to store the text, a copy of the marked-up PDF. As a graduate student in the life sciences, I read and markup a lot of academic papers related to my field.
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